Slide 11 of 27
A minimal sequence of commands to process a dataset would be as follows;
- Autoindex the image (if no spots have already been found, then the program will do this first).
- Estimate Mosaicity: this gives a working value for the mosaicity; it is reliable for images provided there is little thermal diffuse scattering.
- Predict: overlays the predicted spot positions with boxes; always check that the cell and mosaicity found in the previous two steps match the image!
- Beam/backstop: use this to eliminate the area in the backstop shadow from integration.
- Integrate: run an integration on a single image to check on the effective resolution of the data.
- Refine cell: get the best possible fit of calculated to observed spot positions before integrating.
It is normal at this point in the process to close down the GUI and complete processing from the command line or from a command file because these routes are much faster than using the GUI. Mosflm prompts the user to save the current parameters in a file, which can be used in a separate run of Mosflm.
- Integrate: integrate the whole dataset.